eda-merged-bottle-data

Spacial and temporal information

# Load necessary libraries
library(ggplot2)
library(readr)
# read in merged bottle data
merged_bottle_data <- read_csv("../data/merged_bottle_data.csv")

Rows: 461 Columns: 137
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr   (17): EXPOCODE, Ship_Name.x, Station_ID, Depth_ID, Cruise_ID, DbSta_ID...
dbl  (109): Year_UTC, Month_UTC, Day_UTC, Latitude, Longitude, Depth, CTDTEM...
lgl    (3): pH1, pH2, DIC Quality Comment
date   (1): Date
time   (7): Time_UTC, IncTim, Time, Inc_Str, Inc_End, PST_LAN, Civil_T

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# First plot: Date vs Station ID
ggplot(merged_bottle_data, aes(x = Date, y = Station_ID)) +
  geom_point(alpha = 0.5, size = 1) +
  labs(title = "Visualization of Date vs Station ID", x = "Date", y = "Station ID") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

library(mapview)  # For interactive maps
library(sf)       # For spatial data handling

Warning: package 'sf' was built under R version 4.3.3

Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE

library(dplyr)    # For data manipulation

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

# Count the number of observations per Station_ID
station_counts <- merged_bottle_data %>%
  group_by(Station_ID) %>%
  summarise(Observation_Count = n())  # Count occurrences per Station_ID

# Merge the count data back to the original dataset
merged_bottle_ct <- merged_bottle_data %>%
  left_join(station_counts, by = "Station_ID")

# Convert to spatial format using sf 
merged_bottle_sf <- st_as_sf(merged_bottle_ct, 
                             coords = c("Longitude", "Latitude"), 
                             crs = 4326)  # WGS 84 (standard lat/lon system)

# Create an interactive map
mapview(merged_bottle_sf, 
        zcol = "Observation_Count",  # Color by number of observations
        layer.name = "Stations (Observations Count)", 
        legend = TRUE)

Variable descriptions

Sample identifiers

Cst_Cnt: Cast Count - All CalCOFI casts ever conducted, consecutively numbered

Btl_Cnt: Bottle Count - All CalCOFI bottles ever sampled, consecutively numbered

Station_ID: Line and Station [Line] [Station]

Spacial/temporal info

Date: date object (yyyy-mm-dd)

Depthm: Bottle depth in meters

Latitude:

Longitude:

Measurements

from calcofi hydro bottle data:

T_degC: Water temperature in degrees Celsius (degrees Celsius)

Salnty: Salinity (Practical Salinity Scale 1978)

O2ml_L: Milliliters oxygen per liter of seawater

STheta: Potential Density (Sigma Theta) (kilograms per cubic meter)

O2Sat: Oxygen percent saturation

Oxy_ $\mu$ mol/Kg: Oxygen micromoles per kilogram seawater

ChlorA: Migrograms Chlorophyll-a per liter seawater, measured fluorometrically

Phaeop: Micrograms Phaeopigment per liter seawater, measured fluormetrically

PO4uM: Micromoles Phosphate per liter of seawater

SiO3uM: Micromoles Silicate per liter of seawater

NO2uM: Micromoles Nitrite per liter of seawater

NO3uM: Micromoles Nitrate per liter of seawater

NH3uM: Micromoles Ammonia per liter of seawater

DIC1: Dissolved Inorganic Carbon micromoles per kilogram solution

DIC2: Dissolved Inorganic Carbon micromoles per kilogram solution (on a replicate sample)

TA1: Total Alkalinity micromoles per kilogram solution

TA2: Total Alkalinity micromoles per kilogram solution (on a replicate sample)

pH1: pH (the degree of acidity/alkalinity of a solution)

pH2: pH (the degree of acidity/alkalinity of a solution) on a replicate sample

(Obtained from: https://calcofi.org/data/oceanographic-data/bottle-database/)

from carbonate chemistry data:

Dissolved Inorganic Carbon
Abbreviation:
Unit:

Total alkalinity
Abbreviation:
Unit:

Sea water practical salinity
Abbreviation:
Unit:

Sea water temperature
Abbreviation:
Unit:

(Citation: Keeling, Charles D.; Lueker, Timothy J.; Emanuele, Guy; Dickson, Andrew G.; Martz, Todd R.; Wolfe, Wiley H.; Mau, Aaron (2025). Discrete profile dissolved inorganic carbon, total alkalinity, water temperature and salinity measurements collected and assembled from a number of cruises on many different ships for the California Cooperative Oceanic Fisheries Investigations program (CalCOFI) in the North East Pacific Ocean Coastal area from 1983-03-19 to 2021-07-20 (NCEI Accession 0301029). NOAA National Centers for Environmental Information. Unpublished Dataset. https://www.ncei.noaa.gov/archive/accession/0301029. Accessed Jan 2nd 2025.)